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The Biology and Function of Tissue Inhibitor of Metalloproteinase 2 in the Lungs. Pulm Med 2022; 2022:3632764. [PMID: 36624735 PMCID: PMC9825218 DOI: 10.1155/2022/3632764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 01/02/2023] Open
Abstract
Tissue inhibitors of matrix metalloproteinases (TIMP) are a family of four endogenous proteins that primarily function to inhibit the activities of proteases such as the matrix metalloproteinases (MMP). Altered MMP/TIMP ratios are frequently observed in several human diseases. During aging and disease progression, the extracellular matrix (ECM) undergoes structural changes in which elastin and collagens serve an essential role. MMPs and TIMPs significantly influence the ECM. Classically, elevated levels of TIMPs are suggested to result in ECM accumulation leading to fibrosis, whereas loss of TIMP responses leads to enhanced matrix proteolysis. Here, we outline the known roles of the most abundant TIMP, TIMP2, in pulmonary diseases but also discuss future perspectives in TIMP2 research that could impact the lungs. TIMP2 directly inhibits MMPs, in particular MMP2, but TIMP2 is also required for the activation of MMP2 through its interaction with MMP14. The protease and antiprotease imbalance of MMPs and TIMPs are extensively studied in diseases but recent discoveries suggest that TIMPs, specifically, TIMP2 could play other roles in aging and inflammation processes.
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Kim W, Hecker J, Barr RG, Boerwinkle E, Cade B, Correa A, Dupuis J, Gharib SA, Lange L, London SJ, Morrison AC, O'Connor GT, Oelsner EC, Psaty BM, Vasan RS, Redline S, Rich SS, Rotter JI, Yu B, Lange C, Manichaikul A, Zhou JJ, Sofer T, Silverman EK, Qiao D, Cho MH. Assessing the contribution of rare genetic variants to phenotypes of chronic obstructive pulmonary disease using whole-genome sequence data. Hum Mol Genet 2022; 31:3873-3885. [PMID: 35766891 PMCID: PMC9652112 DOI: 10.1093/hmg/ddac117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/13/2022] [Accepted: 05/16/2021] [Indexed: 01/04/2023] Open
Abstract
RATIONALE Genetic variation has a substantial contribution to chronic obstructive pulmonary disease (COPD) and lung function measurements. Heritability estimates using genome-wide genotyping data can be biased if analyses do not appropriately account for the nonuniform distribution of genetic effects across the allele frequency and linkage disequilibrium (LD) spectrum. In addition, the contribution of rare variants has been unclear. OBJECTIVES We sought to assess the heritability of COPD and lung function using whole-genome sequence data from the Trans-Omics for Precision Medicine program. METHODS Using the genome-based restricted maximum likelihood method, we partitioned the genome into bins based on minor allele frequency and LD scores and estimated heritability of COPD, FEV1% predicted and FEV1/FVC ratio in 11 051 European ancestry and 5853 African-American participants. MEASUREMENTS AND MAIN RESULTS In European ancestry participants, the estimated heritability of COPD, FEV1% predicted and FEV1/FVC ratio were 35.5%, 55.6% and 32.5%, of which 18.8%, 19.7%, 17.8% were from common variants, and 16.6%, 35.8%, and 14.6% were from rare variants. These estimates had wide confidence intervals, with common variants and some sets of rare variants showing a statistically significant contribution (P-value < 0.05). In African-Americans, common variant heritability was similar to European ancestry participants, but lower sample size precluded calculation of rare variant heritability. CONCLUSIONS Our study provides updated and unbiased estimates of heritability for COPD and lung function, and suggests an important contribution of rare variants. Larger studies of more diverse ancestry will improve accuracy of these estimates.
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Affiliation(s)
- Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Julian Hecker
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - R Graham Barr
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University of Public Health, Boston, MA 02118, USA
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Leslie Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Alanna C Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - George T O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Elizabeth C Oelsner
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Departments of Epidemiology and Health Services, University of Washington, Seattle, WA 98101, USA
| | - Ramachandran S Vasan
- Lung and Blood Institute Framingham Heart Study, Boston University and National Heart, Framingham, MA 01702, USA
- Department of Preventive Medicine and Epidemiology, School of Medicine and Public Health, Boston University, Boston, MA 02118, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Christoph Lange
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jin J Zhou
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ 85721, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorder, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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Abstract
PURPOSE OF REVIEW LDL receptor-related protein 1 (LRP1) is a multifunctional protein with endocytic and signal transduction properties due to its interaction with numerous extracellular ligands and intracellular proteins. This brief review highlights key developments in identifying novel functions of LRP1 in liver, lung, and the central nervous system in disease pathogenesis. RECENT FINDINGS In hepatocytes, LRP1 complexes with phosphatidylinositol 4-phosphate 5-kinase-1 and its related protein to maintain intracellular levels of phosphatidylinositol (4,5) bisphosphate and preserve lysosome and mitochondria integrity. In contrast, in smooth muscle cells, macrophages, and endothelial cells, LRP1 interacts with various different extracellular ligands and intracellular proteins in a tissue-dependent and microenvironment-dependent manner to either enhance or suppress inflammation, disease progression or resolution. Similarly, LRP1 expression in astrocytes and oligodendrocyte progenitor cells regulates cell differentiation and maturation in a developmental-dependent manner to modulate neurogenesis, gliogenesis, and white matter repair after injury. SUMMARY LRP1 modulates metabolic disease manifestation, inflammation, and differentiation in a cell-dependent, time-dependent, and tissue-dependent manner. Whether LRP1 expression is protective or pathogenic is dependent on its interaction with specific ligands and intracellular proteins, which in turn is dependent on the cell type and the microenvironment where these cells reside.
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Affiliation(s)
- Anja Jaeschke
- Department of Pathology and Laboratory Medicine, Metabolic Diseases Research Center, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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He Z, Wang G, Wu J, Tang Z, Luo M. The molecular mechanism of LRP1 in physiological vascular homeostasis and signal transduction pathways. Biomed Pharmacother 2021; 139:111667. [PMID: 34243608 DOI: 10.1016/j.biopha.2021.111667] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/07/2021] [Accepted: 04/23/2021] [Indexed: 01/10/2023] Open
Abstract
Interactions between vascular smooth muscle cells (VSMCs), endothelial cells (ECs), pericytes (PCs) and macrophages (MФ), the major components of blood vessels, play a crucial role in maintaining vascular structural and functional homeostasis. Low-density lipoprotein (LDL) receptor-related protein-1 (LRP1), a transmembrane receptor protein belonging to the LDL receptor family, plays multifunctional roles in maintaining endocytosis, homeostasis, and signal transduction. Accumulating evidence suggests that LRP1 modulates vascular homeostasis mainly by regulating vasoactive substances and specific intracellular signaling pathways, including the plasminogen activator inhibitor 1 (PAI-1) signaling pathway, platelet-derived growth factor (PDGF) signaling pathway, transforming growth factor-β (TGF-β) signaling pathway and vascular endothelial growth factor (VEGF) signaling pathway. The aim of the present review is to focus on recent advances in the discovery and mechanism of vascular homeostasis regulated by LRP1-dependent signaling pathways. These recent discoveries expand our understanding of the mechanisms controlling LRP1 as a target for studies on vascular complications.
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Affiliation(s)
- Zhaohui He
- Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Drug Discovery Reseach Center, Southwest Medical University, 319 Zhongshan Road, Luzhou, Sichuan 646000, China; Department of Clinical Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Gang Wang
- Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Drug Discovery Reseach Center, Southwest Medical University, 319 Zhongshan Road, Luzhou, Sichuan 646000, China; Laboratory for Cardiovascular Pharmacology of Department of Pharmacology, the School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Jianbo Wu
- Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Drug Discovery Reseach Center, Southwest Medical University, 319 Zhongshan Road, Luzhou, Sichuan 646000, China; Laboratory for Cardiovascular Pharmacology of Department of Pharmacology, the School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, United States
| | - Zonghao Tang
- Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Drug Discovery Reseach Center, Southwest Medical University, 319 Zhongshan Road, Luzhou, Sichuan 646000, China; Laboratory for Cardiovascular Pharmacology of Department of Pharmacology, the School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China.
| | - Mao Luo
- Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Drug Discovery Reseach Center, Southwest Medical University, 319 Zhongshan Road, Luzhou, Sichuan 646000, China; Laboratory for Cardiovascular Pharmacology of Department of Pharmacology, the School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China.
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Kwon SB, Ernst J. Learning a genome-wide score of human-mouse conservation at the functional genomics level. Nat Commun 2021; 12:2495. [PMID: 33941776 PMCID: PMC8093196 DOI: 10.1038/s41467-021-22653-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/24/2021] [Indexed: 01/06/2023] Open
Abstract
Identifying genomic regions with functional genomic properties that are conserved between human and mouse is an important challenge in the context of mouse model studies. To address this, we develop a method to learn a score of evidence of conservation at the functional genomics level by integrating information from a compendium of epigenomic, transcription factor binding, and transcriptomic data from human and mouse. The method, Learning Evidence of Conservation from Integrated Functional genomic annotations (LECIF), trains neural networks to generate this score for the human and mouse genomes. The resulting LECIF score highlights human and mouse regions with shared functional genomic properties and captures correspondence of biologically similar human and mouse annotations. Analysis with independent datasets shows the score also highlights loci associated with similar phenotypes in both species. LECIF will be a resource for mouse model studies by identifying loci whose functional genomic properties are likely conserved.
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Affiliation(s)
- Soo Bin Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, CA, USA. .,Computer Science Department, University of California, Los Angeles, CA, USA. .,Department of Computational Medicine, University of California, Los Angeles, CA, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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